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- PDB-7dk9: Crystal structure of DsbA-like protein DR2335 from Deinococcus ra... -

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Basic information

Entry
Database: PDB / ID: 7dk9
TitleCrystal structure of DsbA-like protein DR2335 from Deinococcus radiodurans R1, native protein
ComponentsDSBA domain-containing protein
KeywordsOXIDOREDUCTASE / DsbA / thioredoxin fold / Thiol:disulfide interchange protein
Function / homologyDSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin-like superfamily / oxidoreductase activity / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / DSBA-like thioredoxin domain-containing protein
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.72 Å
AuthorsKim, M.-K. / Zhang, J. / Zhao, L.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2020R1F1A1057780 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of DsbA-like protein DR2335 from Deinococcus radiodurans R1, native protein
Authors: Kim, M.-K. / Zhang, J. / Zhao, L.
History
DepositionNov 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DSBA domain-containing protein
B: DSBA domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8054
Polymers52,6042
Non-polymers2012
Water12,719706
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-22 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.475, 87.389, 63.414
Angle α, β, γ (deg.)90.000, 90.090, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DSBA domain-containing protein


Mass: 26302.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: DR_2335 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RRZ4
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 706 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 295 K / Method: microbatch
Details: Sodium potassium phosphate pH 7.0, 8% w/v PEG 500 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 51343 / % possible obs: 97.2 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.024 / Rrim(I) all: 0.061 / Rsym value: 0.056 / Net I/σ(I): 38.8
Reflection shellResolution: 1.72→1.75 Å / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 7.932 / Num. unique obs: 2628 / CC1/2: 0.954 / Rpim(I) all: 0.089 / Rrim(I) all: 0.204 / Rsym value: 0.182

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.72→31.51 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.54 / Phase error: 20.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2201 1960 3.85 %
Rwork0.1776 49006 -
obs0.1793 50966 96.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.46 Å2 / Biso mean: 15.6404 Å2 / Biso min: 2.9 Å2
Refinement stepCycle: final / Resolution: 1.72→31.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3381 0 12 706 4099
Biso mean--31.71 23.54 -
Num. residues----423
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.72-1.760.24411350.16983432356794
1.76-1.810.23371430.17333592373599
1.81-1.860.23361440.1863555369998
1.86-1.920.32011240.27933211333589
1.92-1.990.24631350.22443419355494
1.99-2.070.25321450.2113436358195
2.07-2.160.24361430.18723531367497
2.16-2.280.29281270.21553436356394
2.28-2.420.18971460.17563579372599
2.42-2.610.23181470.177736163763100
2.61-2.870.22481490.17536503799100
2.87-3.280.21361510.167136313782100
3.28-4.130.17921250.14793223334888
4.14-31.510.16741460.138236953841100

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